In the United States, colorectal cancer (CRC) is the third most prevalent and the second most deadly cancer in both sexes. Jemal et al., 58 CANCER J. FOR CLINICIANS 71-96 (2008). CRC is highly curable in its early, localized stages, with a 5-year survival rate exceeding 90%. Id. Unfortunately, 61% of new cases are already advanced at the time of diagnosis. Id. Delayed diagnosis occurs due to the asymptomatic nature of most early-stage CRCs; thus, the key to reducing deaths from CRC is periodic screening of the entire colon in the average risk population. Kahi et al., 135 GASTROENTEROLOGY 380-99 (2008). The current gold standard method for screening is colonoscopy. Id. However, invasive screening modalities, including colonoscopy, are not ideal for application to the asymptomatic population. Therefore, active investigations are now underway to discover noninvasive biomarkers, such as those found in stool, which could supplement or supplant colonoscopic screening.
Hypermethylation of CpG islands (CGIs) is a promising CRC biomarker with high potential for translation into non-invasive CRC detection modalities. CGI hypermethylation is a common epigenetic DNA abnormality that has been strongly linked to CRC. Fraga et al., 23 TRENDS IN GEN. 413-18 (2007). CGI hypermethylation possesses several advantages as a biomarker: 1) hypermethylation at multiple CGIs often exists in adenomas, suggesting its potential utility in early detection (Kim et al., 45 GENES, CHROMOSOMES & CANCER 781-89 (2006)); 2) only one assay per locus is generally needed, in contrast to gene mutation, which frequently require multiple assays due to the presence of mutational hotspots; and 3) quantitative methylation assays are applicable to low-integrity DNA commonly encountered in clinical specimens (Uhlmann et al., 23 ELECTROPHORESIS 4072-79 (2002); Fads et al., 28 NUCL. ACIDS RES. E32 (2000)). However, known cancer-specific methylation targets in the colon have in the past been identified based on their functional relevance to neoplastic progression, rather than on their merit as biomarkers, partly due to the previous lack of genome-wide, high-resolution methodologies for the direct analysis of methylation.
Recent technological advances now offer the ability to perform high-throughput, direct assays of DNA methylation. See Estecio et al., 17 GENOME RES. 1529-36 (2007). In this study, loyed a microarray-based direct scanning assay of DNA methylation to extensively search for CGI hypennethylation events, based purely on their performance as CRC biomarkers, for ultimate application to the average-risk population.